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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature (RNA-seq)

ABSTRACT: We report the application of high-throughput sequencing to performed the p53 regulated trancriptome in HCT116 colon cancer cells treated with the DNA damage 5FU. To study the direct targets of p53 we performed ChIP-seq to deterrmined the p53 biding sites and associated with the expression levels. With this study we identified the new genomic regions regulated by p53 and with special attention in those regions that are non coding and are differentially expressed by the DNA damage drug. Description of the p53 transcriptome in HCT116 colon cancer cell line. The RNA-seq libraries were prepared from purified poly-A+ RNA from untreated and 5-Fluorouracil treated p53 +/+ HCT116 cells for 4 and 12h, including two independent samples for the time 12h. Paired-end and strand specific RNA sequencing libraries were prepared according to Illumina instructions and sequenced on HiSeq 2000 (Ilumina) with sequence length of 150 bp. Raw sequencing data were alignment to the human genome (hg19) using Tophat mapper.

ORGANISM(S): Homo sapiens

SUBMITTER: Maite Huarte

PROVIDER: E-GEOD-58507 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature (expression)

Project description:We report the application of high-throughput sequencing to performed the p53 regulated trancriptome in HCT116 colon cancer cells treated with the DNA damage 5FU. To study the direct targets of p53 we performed ChIP-seq to deterrmined the p53 biding sites and associated with the expression levels. With this study we identified the new genomic regions regulated by p53 and with special attention in those regions that are significally expressed by DNA damage and and are non- coding. HCT116 p53 wt cell transfected with the ASO-SC, ASO lncRNA-1 and ASO unassigned-1 for depletion of this new lncRNAs and treated with the DNA damage drug 5FU for 12h were analyzed in the affimetrix platform HTA2.

2014-12-22 | E-GEOD-58409 | biostudies-arrayexpress

Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature (expression)

2014-12-22 | GSE58409 | GEO

Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature (RNA-seq)

Project description:We report the application of high-throughput sequencing to performed the p53 regulated trancriptome in HCT116 colon cancer cells treated with the DNA damage 5FU. To study the direct targets of p53 we performed ChIP-seq to deterrmined the p53 biding sites and associated with the expression levels. With this study we identified the new genomic regions regulated by p53 and with special attention in those regions that are non coding and are differentially expressed by the DNA damage drug.

2014-12-22 | GSE58507 | GEO

Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature (ChIP-seq)

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p53-dependent regulation of gene expression following DNA damage

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